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WO2018200380A8 - Compositions et procédés d'amélioration de l'identification d'échantillons dans des bibliothèques indexées d'acides nucléiques - Google Patents

Compositions et procédés d'amélioration de l'identification d'échantillons dans des bibliothèques indexées d'acides nucléiques Download PDF

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Publication number
WO2018200380A8
WO2018200380A8 PCT/US2018/028867 US2018028867W WO2018200380A8 WO 2018200380 A8 WO2018200380 A8 WO 2018200380A8 US 2018028867 W US2018028867 W US 2018028867W WO 2018200380 A8 WO2018200380 A8 WO 2018200380A8
Authority
WO
WIPO (PCT)
Prior art keywords
compositions
nucleic acid
methods
sample identification
indexed nucleic
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
Application number
PCT/US2018/028867
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English (en)
Other versions
WO2018200380A1 (fr
Inventor
Eric Hans Vermaas
Mahdieh Khosroheidari
Angela KALBANDE
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Illumina Cambridge Ltd
Illumina Inc
Original Assignee
Illumina Cambridge Ltd
Illumina Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority to CA3060979A priority Critical patent/CA3060979C/fr
Priority to ES18723273T priority patent/ES2893528T3/es
Priority to DK18723273.1T priority patent/DK3615690T3/da
Priority to SG11201909918X priority patent/SG11201909918XA/en
Priority to CN201880042176.XA priority patent/CN111094584B/zh
Priority to EP21168956.7A priority patent/EP3872187B1/fr
Application filed by Illumina Cambridge Ltd, Illumina Inc filed Critical Illumina Cambridge Ltd
Priority to EP18723273.1A priority patent/EP3615690B1/fr
Priority to AU2018260627A priority patent/AU2018260627B2/en
Publication of WO2018200380A1 publication Critical patent/WO2018200380A1/fr
Anticipated expiration legal-status Critical
Publication of WO2018200380A8 publication Critical patent/WO2018200380A8/fr
Ceased legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates
    • C12Q1/6855—Ligating adaptors
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869—Methods for sequencing
    • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B20/00—Methods specially adapted for identifying library members
    • C40B20/04—Identifying library members by means of a tag, label, or other readable or detectable entity associated with the library members, e.g. decoding processes
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00—Libraries per se, e.g. arrays, mixtures
    • C40B40/04—Libraries containing only organic compounds
    • C40B40/06—Libraries containing nucleotides or polynucleotides, or derivatives thereof
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B50/00—Methods of creating libraries, e.g. combinatorial synthesis
    • C40B50/06—Biochemical methods, e.g. using enzymes or whole viable microorganisms
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B70/00—Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B80/00—Linkers or spacers specially adapted for combinatorial chemistry or libraries, e.g. traceless linkers or safety-catch linkers

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Zoology (AREA)
  • Engineering & Computer Science (AREA)
  • Wood Science & Technology (AREA)
  • Analytical Chemistry (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • Immunology (AREA)
  • Biotechnology (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

La présente invention concerne des compositions et des procédés d'amélioration du taux d'identification correcte d'échantillons dans des préparations de bibliothèques indexées d'acides nucléiques pour un séquençage multiplex de nouvelle génération par traitement par exonucléase après que des adaptateurs de protection ont été ligaturés à des polynucléotides cibles pour dégrader des adaptateurs non incorporés avant amplification et séquençage.
PCT/US2018/028867 2017-04-23 2018-04-23 Compositions et procédés d'amélioration de l'identification d'échantillons dans des bibliothèques indexées d'acides nucléiques Ceased WO2018200380A1 (fr)

Priority Applications (8)

Application Number Priority Date Filing Date Title
ES18723273T ES2893528T3 (es) 2017-04-23 2018-04-23 Composiciones y métodos para mejorar la identificación de muestras en colecciones de ácidos nucleicos indexadas
DK18723273.1T DK3615690T3 (da) 2017-04-23 2018-04-23 Sammensætninger og fremgangsmåder til forbedring af prøveidentificering i indekserede nukleinsyrebiblioteker
SG11201909918X SG11201909918XA (en) 2017-04-23 2018-04-23 Compositions and methods for improving sample identification in indexed nucleic acid libraries
CN201880042176.XA CN111094584B (zh) 2017-04-23 2018-04-23 用于改进编索引的核酸文库中的样品鉴定的组合物和方法
EP21168956.7A EP3872187B1 (fr) 2017-04-23 2018-04-23 Compositions et procédés d'amélioration de l'identification d'échantillons dans des bibliothèques indexées d'acides nucléiques
CA3060979A CA3060979C (fr) 2017-04-23 2018-04-23 Compositions et procedes d'amelioration de l'identification d'echantillons dans des bibliotheques indexees d'acides nucleiques
EP18723273.1A EP3615690B1 (fr) 2017-04-23 2018-04-23 Compositions et procédés d'amélioration de l'identification d'échantillons dans des bibliothèques indexées d'acides nucléiques
AU2018260627A AU2018260627B2 (en) 2017-04-23 2018-04-23 Compositions and methods for improving sample identification in indexed nucleic acid libraries

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201762488830P 2017-04-23 2017-04-23
US62/488,830 2017-04-23

Publications (2)

Publication Number Publication Date
WO2018200380A1 WO2018200380A1 (fr) 2018-11-01
WO2018200380A8 true WO2018200380A8 (fr) 2019-12-05

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2018/028867 Ceased WO2018200380A1 (fr) 2017-04-23 2018-04-23 Compositions et procédés d'amélioration de l'identification d'échantillons dans des bibliothèques indexées d'acides nucléiques

Country Status (10)

Country Link
US (1) US10995369B2 (fr)
EP (2) EP3615690B1 (fr)
CN (1) CN111094584B (fr)
AU (1) AU2018260627B2 (fr)
CA (1) CA3060979C (fr)
DK (2) DK3872187T3 (fr)
ES (2) ES2929837T3 (fr)
FI (1) FI3872187T3 (fr)
SG (1) SG11201909918XA (fr)
WO (1) WO2018200380A1 (fr)

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US10995369B2 (en) 2021-05-04
FI3872187T3 (fi) 2022-12-15
ES2929837T3 (es) 2022-12-02
DK3872187T3 (da) 2022-12-05
WO2018200380A1 (fr) 2018-11-01
AU2018260627B2 (en) 2024-08-22
CA3060979A1 (fr) 2018-11-01
EP3872187B1 (fr) 2022-09-21
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